deletion in intron region, any consequences?

Question

[raj.fatema]

hey,

so i did the sequencing for my gene and found a deletion in the intron region. it seems like my sample doesnt have the consensus sequences one wishes to see in the intron and so i dont know if the deletion is deleterious or not.

normally, if a deletion is seen in the intron non-splicing regions, does this suggest any deleterious effects of any kind?

[Bert Overduin]

See this question: Effect Of A Deletion In Intron.

Answer 1

[Devon Ryan]

Knowing nothing else, one would predict that to not be deleterious. However, there are undoubtedly cases where this sort of deletion is deleterious (e.g., deletion of an intronic CTCF binding site could easily lead to pathology). So, if this gene is a very good candidate for reasons, then you might consider looking further into what the deletion might be doing (do look at relevant controls first!). If, on the other hand, you're doing a big screen and this is just one of a number of possible candidates, then I wouldn't put much emphasis on it.

[raj.fatema]

biochemical testing from a well-established clinic has shown that my patient has a certain deficiency, i am trying to find the basis of it by genetic testing. i have sequenced the entire gene and so far this is the only variation i found on comparison with the reference sequences in BLAST. :-s

[Devon Ryan]

Assuming this gene is pivotal in the process in question, the next step would be to see if the deleted region is highly evolutionarily conserved. If it is, then that's a very strong indication that removal may have biological effect. That's a pretty quick thing to do and would be what I'd do before checking matched control patients. Also, check dbSNP and 1000 genomes to ensure that this hasn't been reported before.